Package is installed on startup then deleted as an orphan right away #1538

mkcode · 2015-05-08T20:50:13Z

As per discussion in #1534.

Found 1 new package(s) to install...
--> fetching new package repository indexes...
--> installing avy... [1/1]
Found 1 orphan package(s) to delete...
--> deleting avy... [1/1]

every time spacemacs is restarted.

Thank you, can you open an issue for this,
Seems that we have a regression in 24.5.1, somebody else has another
package (spinner) acting like that.

The text was updated successfully, but these errors were encountered:

syl20bnr · 2015-05-09T14:23:18Z

I cannot reproduce it in my current config and in a stock config in develop.
Can you paste the layers you use ?

mkcode · 2015-05-09T14:47:33Z

(defun dotspacemacs/layers ()
  "Configuration Layers declaration."
  (setq-default
   ;; List of additional paths where to look for configuration layers.
   ;; Paths must have a trailing slash (ie. `~/.mycontribs/')
   dotspacemacs-configuration-layer-path '()
   ;; List of configuration layers to load. If it is the symbol `all' instead
   ;; of a list then all discovered layers will be installed.
   dotspacemacs-configuration-layers
   '(
     ;; --------------------------------------------------------
     ;; Example of useful layers you may want to use right away
     ;; Uncomment a layer name and press C-c C-c to install it
     ;; --------------------------------------------------------
     auto-completion
     better-defaults
     clojure
     (colors :variables
             colors-enable-rainbow-identifiers nil)
     (dash :variables
           dash-at-point-legacy-mode t)
     (git :variables
          git-gutter-use-fringe t
          git-magit-status-fullscreen nil
          git-enable-github-support t)
     gtags
     (html :variables
           css-indent-offset 2
           web-mode-code-indent-offset 2
           web-mode-markup-indent-offset 2
           web-mode-css-indent-offset 2)
     javascript
     lua
     markdown
     org
     osx
     (ruby :variables
           ruby-version-manager 'rbenv
           ruby-enable-ruby-on-rails-support t)
     syntax-checking
     xkcd
     )
   ;; A list of packages and/or extensions that will not be install and loaded.
   dotspacemacs-excluded-packages '()
   ;; If non-nil spacemacs will delete any orphan packages, i.e. packages that
   ;; are declared in a layer which is not a member of
   ;; the list `dotspacemacs-configuration-layers'
   dotspacemacs-delete-orphan-packages nil))

The dotspacemacs-delete-orphan-packages nil is a temporary workaround.

syl20bnr · 2015-05-09T15:52:20Z

I still cannot reproduce it, even when I removed by hand the avy directory from elpa directory. It is correctly reinstalled without being deleted.

syl20bnr · 2015-05-09T15:52:55Z

What's the output of (emacs-version) ?

mkcode · 2015-05-09T16:05:54Z

emacs-version

GNU Emacs 24.5.1 (x86_64-apple-darwin14.1.0, Carbon Version 157 AppKit 1344.72)

hmm - and it was built using the railwaycat home-brew version with xml2

brew install emacs-mac --with-xml2 --with-spacemacs-icon

mkcode · 2015-05-09T16:20:01Z

Just recompiled w/o the xml2 support and it's the same behavior. No change there.

mkcode · 2015-05-09T16:26:36Z

Install log:

$ brew install emacs-mac --with-spacemacs-icon
==> Installing emacs-mac from railwaycat/homebrew-emacsmacport
==> Cloning http://www.math.s.chiba-u.ac.jp/~mituharu/emacs-mac.git
Updating /Library/Caches/Homebrew/emacs-mac--git
==> Checking out revision emacs-24.5-mac-5.7
######################################################################## 100.0%
==> ./autogen.sh
==> ./configure --prefix=/usr/local/Cellar/emacs-mac/emacs-24.5-z-mac-5.7 --enable-locallisppath=/usr/local/share/emacs/site-lisp --infodir=/usr/local/Cellar/emacs-mac/emacs-24.5-z-mac-5.7/share/info/emacs --
==> make
==> make install

mkcode · 2015-05-09T16:55:29Z

Just tried with the non-railwaycat regular emacs version and same behavior again.

emacs-version

"GNU Emacs 24.5.1 (x86_64-apple-darwin14.1.0, NS apple-appkit-1344.72)

installed via

brew install emacs --with-cocoa

syl20bnr · 2015-05-09T17:00:32Z

It's getting weird. The only difference with me is that I build with emacs --with-x11 and few other dependencies for image support. But I don't see why such deps would trigger such issue.

To be sure, did you test with fresh cloned Emacs in develop branch ?

mkcode · 2015-05-09T17:28:26Z

Ok! Found the issue!

rm -rf elpa and restarting fixed this. Looks like I did not update the packages... ugg...

this should always be our first goto when someone has a package issue.

so glad I went on a compiling spree for this...

apologies for the waste of time.

syl20bnr · 2015-05-09T17:35:03Z

Excellent thank you for finding the fix.

When you update, do you update with the [update] button on the start page ?

But I wonder how it is possible to end up in your situation. What I
understand is that a package is detected to be installed but the index of
repositories (which contains the denpendencies) is not updated.
I have not check where is the error. At first glance I don't see it in
Spacemacs because if it was he case them it should happen only once.

Le samedi 9 mai 2015, Chris Ewald notifications@github.com a écrit :

Ok! Found the issue!

rm -rf elpa and restarting fixed this. Looks like I did not update the
packages... ugg...

this should always be our first goto when someone has a package issue.

so glad I went on a compiling spree for this...

—
Reply to this email directly or view it on GitHub
#1538 (comment)
.

-syl20bnr-

mkcode · 2015-05-09T17:39:34Z

I believe Spacemacs updates packages when the version changes but not when a user is on the develop branch, yes? If so, that is the issue. I am on the develop branch and and just simply did not update the packages.

Rolling back and then hitting the update button fixes this as well.

mkcode · 2015-05-09T18:14:09Z

@syl20bnr - found the issue:

This commit: 77b0cc4

brought in the ace-link package which does not include avy in the melpa dependencies, but requires it here:

https://github.com/abo-abo/ace-link/blob/master/ace-link.el#L39

mkcode · 2015-05-09T18:27:32Z

@syl20bnr - found the issue:

This commit: 77b0cc4

brought in the ace-link package which does not include avy in the melpa dependencies, but requires it here:

https://github.com/abo-abo/ace-link/blob/master/ace-link.el#L39

this is wrong. nevermind. Not sure what could cause this.

syl20bnr · 2015-05-09T18:44:08Z

The only explanations I can see are:

for some reason spacemacs did not succeed in updating the archives in ~/.emacs.d/elpa/archives
there was a conflict between two archives where the specified package is present.

syl20bnr · 2015-05-09T18:52:10Z

@mkcode are you sure it is fixed ? did you revert back dotspacemacs-delete-orphan-packages to t ?

mkcode · 2015-05-09T19:09:30Z

@syl20bnr - yes. dotspacemacs-delete-orphan-packages is t

Restarting no longer causes this.

syl20bnr · 2015-05-09T19:37:07Z

Tell me if I understand correctly what happened.
You never updated the packages and at one point, without doing anything you got the issue with avy that's it ?

mkcode · 2015-05-09T19:48:13Z

I was on develop branch. pulled latest changes. then the issue appeared. never updated.

syl20bnr · 2015-05-09T19:50:23Z

Can you paste the content of git reflog in your repo ?

mkcode · 2015-05-09T19:56:16Z

bc034b5 HEAD@{0}: merge camel-case-motion: Merge made by the 'recursive' strategy.
a740923 HEAD@{1}: checkout: moving from develop to dev
a740923 HEAD@{2}: checkout: moving from a740923dd9b47238b0f6cd9518bbfafd68176be7 to develop
a740923 HEAD@{3}: checkout: moving from master to origin/develop
ae343bb HEAD@{4}: pull: Fast-forward
1ab8841 HEAD@{5}: checkout: moving from dev to master
35ffb4a HEAD@{6}: merge camel-case-motion: Merge made by the 'recursive' strategy.
a740923 HEAD@{7}: checkout: moving from develop to dev
a740923 HEAD@{8}: pull origin develop: Fast-forward
68ab964 HEAD@{9}: checkout: moving from dev to develop
92df9bd HEAD@{10}: checkout: moving from fix-helm-window to dev
a3faf0b HEAD@{11}: checkout: moving from a3faf0b53b8b39eb50192d00e76e2ce5ff1a4173 to fix-helm-window
a3faf0b HEAD@{12}: checkout: moving from dev to gh-tuhdo/helm-window-fix
92df9bd HEAD@{13}: merge a3faf0b53b8b39e: Merge made by the 'recursive' strategy.
baa9f80 HEAD@{14}: reset: moving to HEAD~1
3e0f291 HEAD@{15}: merge gh-tuhdo/helm-window-fix: Merge made by the 'recursive' strategy.
baa9f80 HEAD@{16}: merge camel-case-motion: Merge made by the 'recursive' strategy.
f9cab4f HEAD@{17}: merge describe-bindings: Fast-forward
68ab964 HEAD@{18}: checkout: moving from describe-bindings to dev
f9cab4f HEAD@{19}: commit: set key "hdb" to describe-bindings
68ab964 HEAD@{20}: checkout: moving from dev to describe-bindings
68ab964 HEAD@{21}: checkout: moving from develop to dev
68ab964 HEAD@{22}: rebase finished: returning to refs/heads/develop
68ab964 HEAD@{23}: pull --rebase origin develop: checkout 68ab964405f9d277c4d348f6339312fcc80ac07f
81706ba HEAD@{24}: checkout: moving from dev to develop
81706ba HEAD@{25}: checkout: moving from develop to dev
81706ba HEAD@{26}: checkout: moving from camel-case-motion to develop
2475457 HEAD@{27}: commit: add CamelCase motion toggle and with subword-mode hook
81706ba HEAD@{28}: checkout: moving from develop to camel-case-motion
81706ba HEAD@{29}: rebase finished: returning to refs/heads/develop
81706ba HEAD@{30}: pull --rebase origin develop: checkout 81706ba6c5f6e1af086c763c48c208fcd02c5dd3

there is a bunch of noise in that, where I use a dev local branch and merge some features that are not upstream.

mkcode · 2015-05-09T20:00:53Z

Note that this occurred after

a740923 HEAD@{2}: checkout: moving from a740923dd9b47238b0f6cd9518bbfafd68176be7 to develop
a740923 HEAD@{3}: checkout: moving from master to origin/develop
ae343bb HEAD@{4}: pull: Fast-forward

syl20bnr · 2015-05-09T20:28:47Z

Thank you ! I tried these commits and was not able to reproduce it, so this have to do with elpa directory and the archives. I hope to be able to reproduce it one day. For now I close it as not reproducible.

trishume · 2015-05-11T14:41:17Z

I had the same issue. Executing configuration-layer/update-packages fixed it.

syl20bnr · 2015-05-11T17:39:48Z

Good news ! On my windows box, I just upgraded to 24.5 and get the issue with avy without doing anything.

I reopen the issue and will investigate tonight.

Fixes #1538

syl20bnr · 2015-05-20T06:08:02Z

Should be fixed in develop, the issue was that the orphans were resolved using package-alist instead of the archive dependencies.

Fixes syl20bnr#1538

kyoDralliam · 2015-10-21T16:00:24Z

I seem to have a similar issue with package 's' on a fresh install of spacemacs (emacs version 24.5.1). I have the following process occuring each time I'm launching emacs :

 (Bootstrap) Installing s...
 Found 1 orphan package(s) to delete...
 --> deleting s... [1/1]'''

d12frosted · 2015-10-21T16:02:52Z

The same with emacs-24.3.1 on Ubuntu 14.04, emacs-24.4.1 on Ubuntu 15.04. Master branch of Spacemacs.

michaellee · 2015-10-22T02:09:22Z

I'm experiencing the same thing, package 's' on a fresh install of spacemacs (emacs 24.3.1) on Ubuntu 14.04

d12frosted · 2015-10-22T06:11:36Z

Ah, but on OS X I have never experienced this before.

neutralevil · 2015-10-26T02:40:50Z

I have the same issue with package 's' (emacs-24.5.1 on Windows 7).

d12frosted · 2015-10-26T05:34:04Z

AFAIK, fixed on develop branch

batisteo · 2015-10-30T18:59:39Z

Same on a fresh install of emacs-24.5.1, spacemacs master, Fedora 22.

awesom3o · 2015-11-01T21:36:11Z

same issue here, emacs 24.5.1 & spacemacs master.

TheBB · 2015-11-04T13:30:02Z

We are tracking this is #3534. It will be fixed by PR #3663.

mikowiec · 2016-05-16T16:24:29Z

windows 7
emacs-25.0.92.1
spacemacs-0.105.20
The issue detected. It's imposible to install, after restart del.

rojaster · 2016-07-20T16:51:02Z

I have the same bug. After restarting my installed package was deleted.
ubuntu 15.10
emacs 24.5.1
spacemacs-0.105.21

kandelvijaya · 2016-11-15T19:38:58Z

This happened to me on mac OS Sierra.

tidux · 2016-12-04T09:39:04Z

This is happening to me on Debian Jessie with adoc-mode, although not on newer versions of Emacs on Arch Linux or Windows. Arch is displaying the same behavior with mingus.

qzhao2007 · 2017-01-16T07:55:18Z

I still meet this issue with emacs 25.1 on mac os seirra, and set dotspacemacs-delete-orphan-packages nil also not work.

tsoernes · 2017-07-20T01:46:04Z

I get this error, with Spacemacs 25.2.1, on Fedora 26 x64, with the package dante https://github.com/jyp/dante
Here's my .spacemacs
spacemacs.txt

d12frosted · 2017-07-23T09:50:28Z

@tsoernes you install dante inside of dotspacemacs/user-config by using use-package. While this is nice, you also have dotspacemacs-install-packages set to 'used-only which means that Spacemacs will uninstall any package 'unknown' to layer system. In order to avoid this you have following solutions:

Create private layer and configure dante there
Add dante to dotspacemacs-additional-packages
Set dotspacemacs-install-packages to 'used-but-keep-unused

sunyta2 · 2019-10-27T08:14:55Z

dear, d12frosted.
Set dotspacemacs-install-packages 'used-but-keep-unused
Greatly worked!!!
Thank you so much! d12frosted

mcp292 · 2022-02-28T01:20:29Z

I had the same question. This post in the FAQ solved it, kindly linked here: #8776 (comment).

mkcode mentioned this issue May 8, 2015

Replace ace-jump-mode with avy #1534

Closed

syl20bnr added the <=(- UBO -)=> label May 9, 2015

syl20bnr changed the title ~~Orphan packages regression in Emacs 24.5.1~~ Package is installed on startup then deleted as an orphan right away May 9, 2015

syl20bnr added the Not reproducible x_x label May 9, 2015

syl20bnr closed this as completed May 9, 2015

syl20bnr added a commit that referenced this issue May 20, 2015

Use archive instead of package-alist to detect orphans

0a71214

Fixes #1538

syl20bnr added Bug :-( Fixed in develop and removed <=(- UBO -)=> labels May 20, 2015

robbyoconnor pushed a commit to robbyoconnor/spacemacs that referenced this issue May 21, 2015

Use archive instead of package-alist to detect orphans

7d30576

Fixes syl20bnr#1538

syl20bnr closed this as completed Jun 1, 2015

syl20bnr removed the Fixed in develop label Jun 1, 2015

QiBaobin mentioned this issue Jun 10, 2015

spacemacs/ace-buffer-links: Symbol's function definition is void: ali-generic #1924

Closed

kryptt pushed a commit to kryptt/spacemacs that referenced this issue Sep 6, 2015

Use archive instead of package-alist to detect orphans

8f60021

Fixes syl20bnr#1538

qzhao2007 mentioned this issue Jan 16, 2017

Reproduce a close issue: Package is installed on startup then deleted as an orphan right away(1538) #8186

Closed

kevindashgit mentioned this issue Feb 2, 2018

compiling error: Symbol's function definition is void: org-link-types marsmining/ox-twbs#44

Closed

Package is installed on startup then deleted as an orphan right away #1538

Package is installed on startup then deleted as an orphan right away #1538

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neutralevil commented Oct 26, 2015

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batisteo commented Oct 30, 2015

awesom3o commented Nov 1, 2015

TheBB commented Nov 4, 2015

mikowiec commented May 16, 2016

rojaster commented Jul 20, 2016

kandelvijaya commented Nov 15, 2016

tidux commented Dec 4, 2016

qzhao2007 commented Jan 16, 2017

tsoernes commented Jul 20, 2017

d12frosted commented Jul 23, 2017

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